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      Genomics and Bioinformatics Resources for Crop Improvement

      research-article
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      Plant and Cell Physiology
      Oxford University Press
      Bioinformatics, Database, Omics resource

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          Abstract

          Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.

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          Most cited references287

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          The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

          The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
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            The Sorghum bicolor genome and the diversification of grasses.

            Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
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              A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

              J. Yu (2002)
              We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
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                Author and article information

                Journal
                Plant Cell Physiol
                pcp
                pcellphys
                Plant and Cell Physiology
                Oxford University Press
                0032-0781
                1471-9053
                April 2010
                8 April 2010
                8 April 2010
                : 51
                : 4
                : 497-523
                Affiliations
                RIKEN Plant Science Center, Yokohama, 230-0045 Japan
                Author notes
                *Corresponding author: E-mail, sinozaki@ 123456rtc.riken.jp ; Fax, +81-45-503-9580
                Article
                pcq021
                10.1093/pcp/pcq027
                2852516
                20208064
                9769b640-f91e-4625-848f-2d00338bc477
                © The Author 2010. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 8 February 2010
                : 1 March 2010
                Categories
                Mini Review

                Plant science & Botany
                bioinformatics,database,omics resource
                Plant science & Botany
                bioinformatics, database, omics resource

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